Abstract

Although comparison of RNA-protein interaction profiles across different conditions
has become increasingly important to understanding the function of RNA-binding proteins
(RBPs), few computational approaches have been developed for quantitative comparison
of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for
quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP,
including a modified MA normalization method and a hidden Markov model, is shown to
be able to effectively identify differential binding regions of RBPs in four CLIP-seq
datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available
at http://qbrc.swmed.edu/software/webcite.